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Real-time PCR Data Markup Language
A new standard for archiving and exchanging real-time PCR data
Steve Lefever On behalf of the RDML consortium
SLIDE 2 qPCR = golden standard for nucleic acids quantification Dedicated and precise instruments needed Different software/output format for each instrument/manufacturer Limits possibility to exchange and reanalyse data RDML
1000 2000 3000 4000 5000 6000 7000 8000 9000 1990 1995 2000 2005 2010
PubMed citations / year
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Birth on September 1st 2005 – Jan Hellemans 2005 – 2007 : Open discussion about RDML January 1st 2008 : start of the RDML consortium April 1st 2008 : RDML joins MIBBI January 12th 2009 : RDML paper accepted in Nucleic Acid Research
History of RDML
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Develops and maintains the RDML data exchange format Key developer group, a member community and supporters 41 supporters and members from 20 different countries
RDML consortium
19 companies 22 academic USA (6) UK (2) Belgium (2) USA (5) UK (3) Germany (3) Sweden (2) Portugal, Austria Switzerland, Israel, Australia, Korea, ... Austria, Switzerland, France Spain, Israel, Canada, ...
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Microarrays MIAME MAGE-ML qPCR MIQE RDML Minimum Information for Biological and Biomedical Investigations http://www.mibbi.org Published in August 2008 by Nature Biotechnology RDML adopted as standard for qPCR experiments
MIBBI
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RDML = Real-time PCR Data Markup Language Universal format to store and exchange qPCR data Structured Based on XML Platform independent Easy to extend Small RDML files
What is RDML?
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samples targets 384-well plates
What is RDML?
RDML file ~ 300 Kb Vermeulen et al. Prognostic gene study in neuroblastoma Excel files ~ 11 Mb
File size reduction
732 64 128
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eXtensible Markup Language Language to store data in a structured manner Defines elements delimited by opening and closing tags Easily extensible
What is XML?
<gene> <symbol>actb</symbol> <function>muscle contraction</function> </gene> <gene> <symbol>actb</symbol> <function>muscle contraction</function> <location>chromosome 7: 5533308-5569941</location> </gene>
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List of experimenters List of targets List of samples List of protocols List of Id’s Documentation Experiments Runs Reactions Datapoints
RDML structure
qPCR data annotation
SLIDE 10 List of experimenters List of targets List of samples List of protocols List of Id’s Documentation Experiments Runs Reactions Datapoints
RDML structure
qPCR data Experiment annotation Multiple experiments per file Standard vocabulary (MIQE)
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List of experimenters List of targets List of samples List of protocols List of Id’s Documentation Experiments Runs Reactions Datapoints
RDML structure
Accession numbers for online repositories or journals
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List of experimenters List of targets List of samples List of protocols List of Id’s Documentation Experiments Runs Reactions Datapoints
RDML structure
Contact information of experimenters
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List of experimenters List of targets List of samples List of protocols List of Id’s Documentation Experiments Runs Reactions Datapoints
RDML structure
Target annotation Oligonucleotide sequences
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List of experimenters List of targets List of samples List of protocols List of Id’s Documentation Experiments Runs Reactions Datapoints
RDML structure
Sample annotation cDNA synthesis
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List of experimenters List of targets List of samples List of protocols List of Id’s Documentation Experiments
RDML structure
Any type of protocol
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List of experimenters List of targets List of samples List of protocols List of Id’s Documentation Experiments
RDML structure
Additional information
SLIDE 17 RDML supporting software
Under development:
More to come
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Website
www.rdml.org Tool for creating RDML files Tool for converting RDML file to .csv files Libraries in Java, C, .NET and PHP
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RDML demonstration
Online generation of an RDML file Importing the RDML file in qBasePlus for analysis Convert RDML file into .csv files
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Conclusion
Data standard for qPCR data Universal and extensible Easy exchange of data Broad acceptance by community Submit data in RDML format to journals www.rdml.org
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Acknowledgements
The RDML consortium Jo Vandesompele Jan Hellemans Filip Pattyn Andreas Untergasser Daniel Przybylski
